Thank you for your feedback, and I concur that it might be difficult to implement, but that's why I'm sharing my idea here, so we can find a way to realize it together! As long as the benefits are worth it, a big implementation might not need to obstruct the realization of the idea.
To address your points:
Amount of U21 players on roster - yes currently most teams do not have enough youngsters. It can be solved to make it an optional competition, so competing teams might not join but rebuilding teams will. Another option is that managers will just purchase/train extra U21 players, as they can help in the cup too. To offset the extra salary for those players, the competition could generate money for wins or just ticket sales.
Minutes/gameshape - One way this could be solved is the minutes played in the U21 club games do not count against the weekly minutes for training/gameshape, like then National team games and B3. Another way, which might be even ideal, is let the minutes count, so the U21 (trainees) will make the 48 minutes in the U21 club games and then just as a backup in the real competition for the full team. We could even change the training system a little, so that players receive training for minutes played in the U21 competition (maybe even all positions). That way, managers don't need to play trainees in real competition games losing them games, but they can play them competitively against other trainees.
Achievements - I think the U21 club competition provides an opportunity for even more achievements, if that's important. I do not really value them, but I don't see a problem in adding extra to replace those that make less sense because of the competition.